Supplemental Materials: Polymethylation Scores for Prenatal Maternal Smoke Exposure Persist Until Age 15 and Are Detected in Saliva

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Supplemental Table 1 - Descriptive statistics of excluded vs included samples with methylation data available from the Fragile and Families and Child Wellbeing study. Samples excluded according to the flow diagram in Main Figure 1

Characteristic	M samples	Final analysis group, M samples = 14991	Not in final analysis group, M samples = 1861
Prenatal maternal smoking	1,685
Not exposed		1,201 (80%)	141 (76%)
Smoke exposed		298 (20%)	45 (24%)
Age at DNA methylation sample	1,685
Age 15		746 (50%)	110 (59%)
Age 9		753 (50%)	76 (41%)
Polymethylation score: coefficients for sustained smoking from newborn cordblood meta-analysis, w/ cell-type control (mean-centered)	1,685	0.00 (0.23)	-0.01 (0.24)
AHHR: cg05575921	1,685	77.1 (5.8)	75.2 (7.4)
Pediatric clock	1,685	10.29 (1.88)	10.52 (1.84)
Global methylation	1,685	47.51 (0.80)	47.42 (0.90)
Immune cell proportion (saliva)	1,685	0.94 (0.13)	0.93 (0.15)
Epithelial cell proportion (saliva)	1,685	0.06 (0.13)	0.07 (0.15)
Ancestry categorization from child principal components of genetic data	1,663
African ancestry		904 (60%)	78 (48%)
European ancestry		235 (16%)	19 (12%)
Hispanic ancestry		360 (24%)	67 (41%)
Unknown		0	22
Child gender	1,685
Boy		740 (49%)	107 (58%)
Girl		759 (51%)	79 (42%)
Maternal prenatal alcohol use	1,681	173 (12%)	20 (11%)
Unknown		0	4
Maternal prenatal any drug use	1,679	73 (4.9%)	11 (6.1%)
Unknown		0	6
Constructed - Poverty ratio - mother's household income/poverty threshold	1,685	2.23 (2.43)	2.35 (2.55)
Any postnatal maternal smoking when child age 1 or 5	1,597
Maternal smoking at age 1 or age 5		590 (39%)	52 (53%)
No maternal smoking at age 1 and 5		909 (61%)	46 (47%)
Unknown		0	88
Maternal/primary care giver smoking in month prior to visit (pks/day)	1,667
Less than pack a day		337 (22%)	42 (25%)
No smoking		1,054 (70%)	115 (68%)
Pack or more a day		108 (7.2%)	11 (6.5%)
Unknown		0	18
1 n (%); Mean (SD)

##    [1] "1000002" "1000005" "1000019" "1000020" "1000024" "1000029" "1000041"
##    [8] "1000042" "1000047" "1000049" "1000052" "1000066" "1000074" "1000084"
##   [15] "1000089" "1000097" "1000099" "1000102" "1000111" "1000129" "1000135"
##   [22] "1000138" "1000186" "1000192" "1000199" "1000201" "1000206" "1000207"
##   [29] "1000223" "1000227" "1000233" "1000236" "1000237" "1000252" "1000254"
##   [36] "1000258" "1000260" "1000271" "1000284" "1000286" "1000291" "1000292"
##   [43] "1000293" "1000294" "1000312" "1000315" "1000316" "1000317" "1000324"
##   [50] "1000326" "1000342" "1000347" "1000361" "1000369" "1000375" "1000378"
##   [57] "1000379" "1000381" "1000389" "1000404" "1000417" "1000418" "1000421"
##   [64] "1000428" "1000429" "1000433" "1000459" "1000475" "1000477" "1000478"
##   [71] "1000484" "1000486" "1000487" "1000488" "1000498" "1000504" "1000507"
##   [78] "1000509" "1000517" "1000538" "1000539" "1000551" "1000552" "1000556"
##   [85] "1000558" "1000560" "1000562" "1000568" "1000580" "1000587" "1000601"
##   [92] "1000603" "1000604" "1000611" "1000622" "1000624" "1000626" "1000627"
##   [99] "1000630" "1000639" "1000653" "1000657" "1000676" "1000680" "1000686"
##  [106] "1000697" "1010204" "1010210" "1010321" "1010387" "1010393" "1010509"
##  [113] "1010771" "1010826" "1010832" "1010848" "1010959" "1011020" "1011153"
##  [120] "1011175" "1011353" "1011369" "1011397" "1011503" "1011842" "1011892"
##  [127] "1012113" "1012535" "1012735" "1012785" "1012907" "1012985" "1013006"
##  [134] "1013206" "1013228" "1013234" "1013345" "1013973" "1013989" "1014016"
##  [141] "1014094" "1014177" "1014199" "1014327" "1014349" "1014511" "1014672"
##  [148] "1014983" "1015004" "1025063" "1025091" "1025130" "1025174" "1025180"
##  [155] "1025263" "1025279" "1025291" "1025318" "1025330" "1025352" "1025479"
##  [162] "1025485" "1025502" "1025530" "1025724" "1025752" "1025796" "1025813"
##  [169] "1025863" "1025885" "1025924" "1026023" "1026039" "1026067" "1026095"
##  [176] "1026106" "1026140" "1026178" "1026190" "1026201" "1026223" "1026251"
##  [183] "1026289" "1026328" "1026340" "1026356" "1026384" "1026417" "1026423"
##  [190] "1026439" "1026451" "1026495" "1026528" "1026590" "1026623" "1026667"
##  [197] "1026706" "1026728" "1026740" "1026756" "1026801" "1026823" "1026839"
##  [204] "1026845" "1026867" "1026895" "1026912" "1026928" "1026934" "1026940"
##  [211] "1026956" "1027005" "1027033" "1027077" "1027138" "1027144" "1027194"
##  [218] "1027205" "1027316" "1027344" "1027388" "1027449" "1027477" "1027499"
##  [225] "1027611" "1027633" "1027649" "1027661" "1027700" "1027738" "1027744"
##  [232] "1028015" "1028021" "1028037" "1028043" "1028093" "1028110" "1028148"
##  [239] "1028160" "1028198" "1028215" "1028221" "1028293" "1028310" "1028354"
##  [246] "1028376" "1028382" "1028415" "1028459" "1028465" "1028471" "1028560"
##  [253] "1028665" "1028710" "1028726" "1028732" "1028754" "1028821" "1028859"
##  [260] "1028893" "1028926" "1028960" "1028982" "1029003" "1029047" "1029097"
##  [267] "1029114" "1029120" "1029142" "1029164" "1029170" "1029203" "1029225"
##  [274] "1029253" "1029275" "1029342" "1029358" "1029847" "1029869" "1029914"
##  [281] "1029920" "1029936" "1029942" "1049021" "1050167" "1050195" "1050240"
##  [288] "1050301" "1050345" "1050478" "1050640" "1050789" "1050917" "1051872"
##  [295] "1051927" "1052232" "1052343" "1052393" "1052454" "1052765" "1052971"
##  [302] "1053070" "1053220" "1053331" "1054135" "1054252" "1054357" "1054496"
##  [309] "1054735" "1065043" "1065093" "1065132" "1065148" "1065459" "1065576"
##  [316] "1065760" "1066081" "1066108" "1066164" "1066231" "1066320" "1066364"
##  [323] "1066508" "1066558" "1066669" "1066675" "1066770" "1066819" "1066920"
##  [330] "1067041" "1067063" "1067091" "1067718" "1067774" "1067835" "1067879"
##  [337] "1067918" "1067924" "1068017" "1068112" "1068156" "1068190" "1068306"
##  [344] "1068467" "1068495" "1069227" "1069455" "1069605" "1069677" "1069699"
##  [351] "1069738" "1069750" "1069877" "1069994" "1088035" "1088041" "1088213"
##  [358] "1088235" "1088479" "1089306" "1089334" "1089401" "1090020" "1090042"
##  [365] "1090070" "1090092" "1090103" "1090119" "1090125" "1090147" "1090303"
##  [372] "1090319" "1090325" "1090347" "1090369" "1090464" "1090547" "1090553"
##  [379] "1090608" "1090614" "1090642" "1090658" "1090703" "1090719" "1090731"
##  [386] "1090775" "1090836" "1090864" "1090892" "1090931" "1090975" "1091191"
##  [393] "1091224" "1091246" "1091424" "1091529" "1091557" "1091624" "1091630"
##  [400] "1091646" "1091846" "1091868" "1092056" "1092101" "1092145" "1092206"
##  [407] "1092212" "1092406" "1092523" "1092545" "1092701" "1092723" "1092739"
##  [414] "1092745" "1092773" "1092828" "1092862" "1092878" "1093022" "1093127"
##  [421] "1093133" "1093149" "1093183" "1093238" "1093250" "1093361" "1093400"
##  [428] "1093438" "1093466" "1093644" "1093672" "1093711" "1093838" "1093850"
##  [435] "1093999" "2000053" "2000561" "2000684" "2001120" "2001463" "2001829"
##  [442] "2002200" "2002886" "2004981" "2005168" "2007344" "2008026" "2008288"
##  [449] "2008330" "2011110" "2011327" "2012559" "2013309" "2016364" "2016623"
##  [456] "2017208" "2017800" "2018469" "2100034" "2100157" "2100322" "2100487"
##  [463] "2100500" "2100898" "2102854" "2102977" "2103196" "2104467" "2105194"
##  [470] "2105356" "2106410" "2200031" "2200141" "2200837" "2201823" "2202644"
##  [477] "2203261" "2203449" "2301176" "2301189" "2303378" "2304199" "2400064"
##  [484] "2400213" "2400307" "2400365" "2400585" "2400828" "2401296" "2401432"
##  [491] "2401678" "2401720" "2401733" "2402017" "2403223" "2403964" "2404280"
##  [498] "2500236" "2500317" "2501170" "2501183" "2501866" "2504041" "2504410"
##  [505] "2506463" "2506670" "2506816" "2506971" "2507116" "2507828" "2507899"
##  [512] "2600026" "2600084" "2600204" "2600576" "2601258" "2601452" "2602312"
##  [519] "2606127" "2606509" "2607634" "2607896" "2609098" "2610281" "2700382"
##  [526] "2700599" "2700861" "2701006" "2701190" "2702131" "2703761" "2703965"
##  [533] "2705170" "2705280" "2705455" "2705675" "2705989" "2706108" "2707709"
##  [540] "2707767" "2707932" "2708164" "2800046" "2800266" "2801896" "2801919"
##  [547] "2802057" "2802277" "2802785" "2804576" "2805355" "2806354" "2806891"
##  [554] "2808284" "2809652" "2900289" "2900331" "2900674" "2902779" "2904230"
##  [561] "3001695" "3008708" "3101029" "3103564" "3104194" "3105614" "3301764"
##  [568] "3302475" "3302734" "3303555" "3304648" "3308291" "3403358" "3506019"
##  [575] "3601024" "4000048" "4000158" "4000187" "4000462" "4000488" "4001704"
##  [582] "4003207" "4005551" "4007575" "4101730" "4103686" "4103880" "4500483"
##  [589] "4502135" "4502850" "4504214" "4504829" "4505394" "4506115" "4506238"
##  [596] "5000186" "5000296" "5001046" "5001428" "5002029" "5002317" "5003222"
##  [603] "5003646" "5004098" "5004975" "5005754" "5100497" "5101166" "5102097"
##  [610] "5102631" "5104189" "5104901" "5105120" "5105285" "5105748" "5108091"
##  [617] "5111046" "5113934" "5116355" "5116672" "5116892" "5202188" "5202447"
##  [624] "5205211" "5205279" "5205318" "5209686" "5212686" "5401167" "5405244"
##  [631] "5500013" "5500026" "5500097" "5500262" "5500314" "5500372" "5500495"
##  [638] "5500602" "5500657" "5502972" "5503405" "5503913" "5503926" "5504019"
##  [645] "5504624" "5504792" "5505199" "5506062" "5600010" "5600049" "5600065"
##  [652] "5600227" "5600256" "5600939" "5602076" "5602351" "5602568" "5602623"
##  [659] "5602940" "5603729" "5603839" "5604061" "5604223" "5604281" "5605248"
##  [666] "6000059" "6000541" "6001032" "6001799" "6100205" "6101495" "6106063"
##  [673] "6106351" "6107431" "6108126" "6109015" "6109060" "6109206" "6200011"
##  [680] "6200312" "6200943" "6201078" "6300157" "6301033" "6301075" "6400264"
##  [687] "6400277" "6401250" "6500290" "6500957" "6501859" "6600022" "6600213"
##  [694] "6600242" "6600268" "6600491" "6600705" "6600857" "6600941" "6601047"
##  [701] "6601953" "6602075" "6602334" "6602745" "6602907" "6700142" "6700757"
##  [708] "6700919" "6701219" "6702577" "6703660" "6800097" "7000281" "7000333"
##  [715] "7001604" "7001659" "7002069" "7002603" "7003055" "7003071" "7003615"
##  [722] "7003644" "7100204" "7101575" "7102079" "7102684" "7103379" "7106211"
##  [729] "7200081" "7200214" "7200285" "7200573" "7201239" "7202775" "7300198"
##  [736] "7300460" "7306710" "7403396" "7500312" "7600115" "7600225" "7601570"
##  [743] "7700154" "7700604" "7701658" "7702013" "7702194" "7703180" "7800588"
##  [750] "7800724" "7800892" "7801189" "7900815" "1000002" "1000005" "1000019"
##  [757] "1000024" "1000029" "1000041" "1000042" "1000047" "1000049" "1000052"
##  [764] "1000066" "1000074" "1000084" "1000089" "1000097" "1000099" "1000111"
##  [771] "1000129" "1000135" "1000138" "1000192" "1000199" "1000201" "1000206"
##  [778] "1000223" "1000227" "1000233" "1000236" "1000237" "1000245" "1000252"
##  [785] "1000254" "1000258" "1000260" "1000284" "1000286" "1000291" "1000293"
##  [792] "1000294" "1000312" "1000315" "1000317" "1000324" "1000326" "1000342"
##  [799] "1000347" "1000361" "1000369" "1000375" "1000378" "1000381" "1000389"
##  [806] "1000404" "1000418" "1000421" "1000428" "1000429" "1000433" "1000459"
##  [813] "1000475" "1000477" "1000478" "1000484" "1000486" "1000487" "1000488"
##  [820] "1000498" "1000504" "1000507" "1000509" "1000517" "1000538" "1000539"
##  [827] "1000551" "1000552" "1000556" "1000558" "1000560" "1000562" "1000568"
##  [834] "1000580" "1000587" "1000601" "1000603" "1000604" "1000611" "1000622"
##  [841] "1000626" "1000627" "1000630" "1000639" "1000653" "1000657" "1000676"
##  [848] "1000686" "1010204" "1010210" "1010321" "1010387" "1010393" "1010509"
##  [855] "1010771" "1010826" "1010832" "1010848" "1010959" "1011020" "1011092"
##  [862] "1011153" "1011175" "1011353" "1011369" "1011397" "1011458" "1011503"
##  [869] "1011842" "1011892" "1012113" "1012513" "1012529" "1012535" "1012785"
##  [876] "1012907" "1012985" "1013006" "1013206" "1013228" "1013234" "1013345"
##  [883] "1013973" "1013989" "1014016" "1014094" "1014177" "1014199" "1014327"
##  [890] "1014349" "1014511" "1014672" "1015004" "1025035" "1025063" "1025091"
##  [897] "1025174" "1025180" "1025263" "1025279" "1025318" "1025330" "1025352"
##  [904] "1025479" "1025485" "1025491" "1025502" "1025524" "1025530" "1025724"
##  [911] "1025752" "1025796" "1025813" "1025835" "1025863" "1025885" "1025924"
##  [918] "1025930" "1025980" "1026023" "1026039" "1026067" "1026095" "1026106"
##  [925] "1026140" "1026178" "1026190" "1026201" "1026223" "1026251" "1026289"
##  [932] "1026328" "1026340" "1026356" "1026362" "1026384" "1026401" "1026417"
##  [939] "1026423" "1026439" "1026451" "1026467" "1026495" "1026528" "1026590"
##  [946] "1026623" "1026645" "1026651" "1026667" "1026706" "1026728" "1026740"
##  [953] "1026756" "1026778" "1026801" "1026823" "1026839" "1026845" "1026867"
##  [960] "1026912" "1026928" "1026940" "1026956" "1026962" "1027005" "1027033"
##  [967] "1027049" "1027077" "1027144" "1027194" "1027205" "1027249" "1027388"
##  [974] "1027449" "1027499" "1027611" "1027633" "1027649" "1027661" "1027700"
##  [981] "1027738" "1028015" "1028021" "1028037" "1028043" "1028110" "1028148"
##  [988] "1028160" "1028182" "1028198" "1028215" "1028221" "1028293" "1028310"
##  [995] "1028354" "1028360" "1028376" "1028382" "1028415" "1028459" "1028465"
## [1002] "1028471" "1028560" "1028665" "1028687" "1028693" "1028710" "1028732"
## [1009] "1028754" "1028821" "1028859" "1028893" "1028960" "1028982" "1029003"
## [1016] "1029047" "1029097" "1029114" "1029120" "1029142" "1029164" "1029170"
## [1023] "1029203" "1029225" "1029253" "1029275" "1029281" "1029342" "1029358"
## [1030] "1029847" "1029869" "1029914" "1029920" "1029936" "1029942" "1049021"
## [1037] "1050167" "1050195" "1050240" "1050301" "1050478" "1050640" "1050789"
## [1044] "1050917" "1051872" "1051927" "1052232" "1052343" "1052393" "1052454"
## [1051] "1052765" "1052971" "1053070" "1053220" "1054135" "1054252" "1054357"
## [1058] "1054735" "1065043" "1065132" "1065148" "1065576" "1065760" "1065776"
## [1065] "1066069" "1066081" "1066108" "1066164" "1066231" "1066320" "1066364"
## [1072] "1066508" "1066536" "1066558" "1066669" "1066675" "1066770" "1066819"
## [1079] "1066920" "1067041" "1067063" "1067091" "1067718" "1067774" "1067835"
## [1086] "1067879" "1067918" "1067924" "1068017" "1068112" "1068190" "1068306"
## [1093] "1068445" "1068467" "1068495" "1069227" "1069455" "1069605" "1069677"
## [1100] "1069699" "1069738" "1069750" "1069877" "1069994" "1088035" "1088041"
## [1107] "1088213" "1088235" "1088479" "1089334" "1089401" "1090020" "1090042"
## [1114] "1090070" "1090092" "1090103" "1090119" "1090147" "1090214" "1090303"
## [1121] "1090319" "1090325" "1090347" "1090369" "1090464" "1090547" "1090553"
## [1128] "1090608" "1090614" "1090642" "1090658" "1090703" "1090719" "1090731"
## [1135] "1090775" "1090836" "1090864" "1090892" "1090931" "1090975" "1091191"
## [1142] "1091224" "1091246" "1091424" "1091529" "1091557" "1091624" "1091630"
## [1149] "1091646" "1091846" "1091868" "1092056" "1092101" "1092145" "1092206"
## [1156] "1092212" "1092406" "1092523" "1092701" "1092723" "1092739" "1092745"
## [1163] "1092773" "1092828" "1092862" "1092878" "1093022" "1093133" "1093149"
## [1170] "1093183" "1093238" "1093250" "1093361" "1093400" "1093438" "1093466"
## [1177] "1093644" "1093672" "1093711" "1093838" "1093850" "1093999" "2000053"
## [1184] "2000561" "2000684" "2001120" "2001463" "2001829" "2002200" "2002886"
## [1191] "2004240" "2004981" "2005168" "2005757" "2007344" "2008026" "2008288"
## [1198] "2008330" "2011110" "2011327" "2012559" "2013309" "2016364" "2016623"
## [1205] "2017208" "2017486" "2017800" "2018469" "2100034" "2100157" "2100322"
## [1212] "2100487" "2100500" "2100898" "2102854" "2102977" "2103196" "2105194"
## [1219] "2105356" "2106410" "2200031" "2200141" "2200837" "2202644" "2203261"
## [1226] "2203449" "2301176" "2301189" "2303378" "2400064" "2400213" "2400307"
## [1233] "2400365" "2400585" "2400828" "2401296" "2401432" "2401678" "2401720"
## [1240] "2401733" "2403223" "2403964" "2500236" "2500317" "2501170" "2501866"
## [1247] "2504410" "2506670" "2506816" "2506971" "2507116" "2507828" "2507899"
## [1254] "2600026" "2600084" "2600204" "2600576" "2601258" "2601452" "2602312"
## [1261] "2606127" "2606509" "2607634" "2607896" "2609098" "2610281" "2700382"
## [1268] "2700599" "2700861" "2701006" "2701190" "2701598" "2702131" "2703761"
## [1275] "2703965" "2705170" "2705280" "2705455" "2705675" "2705989" "2706108"
## [1282] "2707709" "2707767" "2707932" "2708164" "2800046" "2800266" "2801896"
## [1289] "2801919" "2802057" "2802277" "2802785" "2804576" "2806354" "2806891"
## [1296] "2808284" "2809652" "2900137" "2900289" "2900331" "2900593" "2900674"
## [1303] "2902779" "2904230" "2904696" "3001695" "3008708" "3101029" "3103564"
## [1310] "3104194" "3105614" "3301764" "3302475" "3302734" "3303555" "3304648"
## [1317] "3403358" "3506019" "3601024" "4000048" "4000158" "4000462" "4000488"
## [1324] "4000527" "4003207" "4007575" "4101730" "4103686" "4500483" "4502135"
## [1331] "4502850" "4504214" "4504829" "4505394" "4506115" "4506238" "5000296"
## [1338] "5001046" "5001428" "5002029" "5002317" "5003222" "5003646" "5004098"
## [1345] "5004975" "5005754" "5100497" "5102097" "5102631" "5104189" "5104901"
## [1352] "5105120" "5105285" "5105748" "5108091" "5111046" "5113934" "5116355"
## [1359] "5116672" "5116892" "5202188" "5202447" "5205211" "5205279" "5205318"
## [1366] "5212686" "5401167" "5405244" "5500013" "5500026" "5500097" "5500136"
## [1373] "5500262" "5500314" "5500372" "5500495" "5500657" "5500686" "5502972"
## [1380] "5503405" "5503816" "5503913" "5504019" "5504624" "5504637" "5504792"
## [1387] "5505199" "5505872" "5506062" "5506457" "5600010" "5600049" "5600065"
## [1394] "5600227" "5600256" "5600939" "5601695" "5602076" "5602351" "5602568"
## [1401] "5602623" "5602940" "5603729" "5604061" "5604223" "5605248" "6000059"
## [1408] "6000541" "6000619" "6001032" "6001799" "6100205" "6101275" "6101495"
## [1415] "6106351" "6106490" "6106607" "6107431" "6107622" "6108126" "6108223"
## [1422] "6109015" "6109060" "6109206" "6200011" "6200312" "6200943" "6201078"
## [1429] "6300063" "6300157" "6300568" "6301033" "6301075" "6400264" "6400277"
## [1436] "6401250" "6500290" "6500562" "6500957" "6501859" "6600022" "6600213"
## [1443] "6600242" "6600268" "6600491" "6600705" "6600941" "6601047" "6601953"
## [1450] "6602075" "6602334" "6602745" "6700142" "6700919" "6702577" "6702962"
## [1457] "6703660" "6800097" "7000281" "7000333" "7001604" "7001659" "7002069"
## [1464] "7002603" "7003055" "7003071" "7003615" "7003644" "7100204" "7101575"
## [1471] "7102079" "7102684" "7103379" "7106211" "7200081" "7200214" "7200285"
## [1478] "7200573" "7201239" "7300198" "7300460" "7306710" "7403396" "7500312"
## [1485] "7600115" "7600225" "7601570" "7700154" "7700604" "7701658" "7702013"
## [1492] "7702194" "7703180" "7800588" "7800724" "7800892" "7801189" "7900420"
## [1499] "7900815"
## attr(,"label")
## idnum 
##  "ID"

Supplemental Figure 1 - Pearson correlation of selected DNA methylation summary measures from an anlysis of M=1499 samples and N=809children in the Fragile Families and Child Wellbeing cohort. Lower diaganol shows the Pearson rho correlation coefficient, upper triangle shows ellipses illustrating relationship between variables colored by the magnitude and direction of the correlation.

## png 
##   2

Supplemental Figure 2 - Correlation between age 9 and age 15 visit DNA methylation summary measures among 690 children with age 9 and age 15 visit data in the Fragile Families and Child Wellbeing study. Each point represents one individual, x-axis is the DNA methylation summary measure at age 9 and y-axis is the DNA methylation measure at age 15. Blue lines are simple linear regression lines of best fit, with Pearson rho and associated \(P\) value shown. From top-left: Polymethylation score for prenatal maternal smoking, score created using coefficients from a regression of prenatal maternal smoking and DNA methylation in newborn cord blood, incorporating cell-type control. Polymethylation score for prenatal maternal smoking using coefficients from a regression of prenatal maternal smoking and DNA methylation in newborn cord blood, no cell-type control. Polymethylation score calculated using regression coefficients from a regression of prenatal maternal smoking and DNA methylation in older children’s peripheral blood samples. Pediatric epigenetic clock (years). GRIM epigenetic clock (years). Percent DNA methylation at cg05575921 in AHRR. Percent global DNA methylation (mean across all DNA methylation sites in cleaned probe set). Proportion of epithelial cells calculated from DNA methylation using reference panel of children’s saliva. Proportion of immune cells calculated from DNA methylation using a reference panel of children’s saliva.

Supplemental Figure 3: Distributions of selected methylation summary measures at age 9 and age 15 among 809 children in the Fragile Families and Child Wellbeing study. Captive box plots within violin plots show the distribution of selected DNA methylation measures in samples from age 9 (red) and age 15 (blue). Black lines show lines of best fit. From top-left: Polymethylation score for prenatal maternal smoking, score created using coefficients from a regression of prenatal maternal smoking and DNA methylation in newborn cord blood, incorporating cell-type control. Polymethylation score for prenatal maternal smoking using coefficients from a regression of prenatal maternal smoking and DNA methylation in newborn cord blood, no cell-type control. Polymethylation score calculated using regression coefficients from a regression of prenatal maternal smoking and DNA methylation in older children’s peripheral blood samples. Pediatric epigenetic clock (years). GRIM epigenetic clock (years). Percent DNA methylation at cg05575921 in AHRR. Percent global DNA methylation (mean across all DNA methylation sites in cleaned probe set). Proportion of epithelial cells calculated from DNA methylation using reference panel of children’s saliva. Proportion of immune cells calculated from DNA methylation using a reference panel of children’s saliva.

Characteristic	Age 9				Age 15
	N	Not exposed, N = 5981	Smoke exposed, N = 1551	p-value2	N	Not exposed, N = 6031	Smoke exposed, N = 1431	p-value2
Child characteristics
Polymethylation score for smoke exposure	753	-0.04 (0.22)	0.08 (0.22)	<0.001	746	-0.01 (0.22)	0.11 (0.23)	<0.001
AHRR gene: percent cg05575921 methylation	753	77.8 (5.2)	76.8 (5.6)	0.047	746	77 (6)	76 (6)	0.2
Pediatric epigenetic clock (years)	753	8.98 (0.75)	8.94 (0.83)	0.6	746	11.62 (1.75)	11.59 (1.70)	0.9
Percent global DNA methylation	753	47.51 (0.74)	47.59 (0.78)	0.3	746	47.48 (0.85)	47.58 (0.83)	0.2
Immune cell proportion (saliva)	753	0.96 (0.10)	0.96 (0.08)	0.4	746	0.92 (0.15)	0.92 (0.14)	>0.9
Epithelial cell proportion (saliva)	753	0.04 (0.10)	0.04 (0.08)	0.4	746	0.08 (0.15)	0.08 (0.14)	>0.9
Ancestry categorization from child principal components of genetic data	753			0.001	746			0.001
African ancestry		355 (59%)	97 (63%)			364 (60%)	88 (62%)
European ancestry		82 (14%)	35 (23%)			84 (14%)	34 (24%)
Hispanic ancestry		161 (27%)	23 (15%)			155 (26%)	21 (15%)
Child gender	753			0.8	746			0.9
Boy		300 (50%)	76 (49%)			295 (49%)	69 (48%)
Girl		298 (50%)	79 (51%)			308 (51%)	74 (52%)
Maternal characteristics
Maternal prenatal alcohol use	753	44 (7.4%)	47 (30%)	<0.001	746	40 (6.6%)	42 (29%)	<0.001
Maternal prenatal any drug use	753	10 (1.7%)	26 (17%)	<0.001	746	9 (1.5%)	28 (20%)	<0.001
Maternal income to poverty threshold (at baseline)	753	2.41 (2.57)	1.52 (1.56)	<0.001	746	2.41 (2.58)	1.49 (1.57)	<0.001
Postnatal maternal smoking at ages 1 or 5	753			<0.001	746			<0.001
No maternal smoking at age 1 and 5		447 (75%)	7 (4.5%)			448 (74%)	7 (4.9%)
Maternal smoking at age 1 or age 5		151 (25%)	148 (95%)			155 (26%)	136 (95%)
Postnatal primary caregiver smoking in past month prior to visit	753			<0.001	746			<0.001
No smoking		476 (80%)	23 (15%)			511 (85%)	44 (31%)
Less than pack a day		95 (16%)	85 (55%)			80 (13%)	77 (54%)
Pack or more a day		27 (4.5%)	47 (30%)			12 (2.0%)	22 (15%)
1 Mean (SD); n (%) 2 Welch Two Sample t-test; Pearson's Chi-squared test

Supplemental Table 2: Bivariate associations between prenatal maternal smoking and additional DNA methylation summary measures among a diverse sample of 809 children in the Fragile Families and Child Wellbeing study. Percent DNA methylation shown calculated across all DNA methylation sites available (global DNA methylation) and stratified by genomic region (Island, Open Sea, Shelf, Shore). Polymethylation score for smoke exposure from main analysis and from sensitivity analyses where scores were calculated using alternative available regression coefficients.

Characteristic	Age 9				Age 15
	N	Not exposed, N = 5981	Smoke exposed, N = 1551	p-value2	N	Not exposed, N = 6031	Smoke exposed, N = 1431	p-value2
Percent global DNA methylation	753	47.51 (0.74)	47.59 (0.78)	0.3	746	47.48 (0.85)	47.58 (0.83)	0.2
Island methylation	753	18.96 (0.61)	19.06 (0.59)	0.057	746	19.05 (0.61)	19.14 (0.56)	0.10
Open Sea methylation	753	70.36 (1.05)	70.41 (1.11)	0.6	746	70.23 (1.23)	70.35 (1.22)	0.3
Shelf methylation	753	75.33 (1.04)	75.35 (1.10)	0.9	746	75.19 (1.23)	75.30 (1.21)	0.4
Shore methylation	753	44.05 (0.82)	44.16 (0.86)	0.2	746	44.03 (0.94)	44.15 (0.90)	0.2
Pediatric epigenetic clock (years)	753	8.98 (0.75)	8.94 (0.83)	0.6	746	11.62 (1.75)	11.59 (1.70)	0.9
GRIM epigenetic clock (years)	753	24.7 (3.5)	24.5 (3.2)	0.6	746	30.4 (4.0)	30.2 (4.2)	0.6
GRIM pack/yrs component	753	-5.7 (4.7)	-4.7 (5.0)	0.033	746	-4.0 (5.3)	-3.6 (5.1)	0.4
Epithelial cell proportion (saliva)	753	0.04 (0.10)	0.04 (0.08)	0.4	746	0.08 (0.15)	0.08 (0.14)	>0.9
Immune cell proportion (saliva)	753	0.96 (0.10)	0.96 (0.08)	0.4	746	0.92 (0.15)	0.92 (0.14)	>0.9
Polymethylation score for smoke exposure	753	-0.04 (0.22)	0.08 (0.22)	<0.001	746	-0.01 (0.22)	0.11 (0.23)	<0.001
Polymethylation score: coefficients for sustained smoking from newborn cordblood meta-analysis (mean-centered)	753	-0.06 (0.29)	0.05 (0.27)	<0.001	746	0.01 (0.31)	0.12 (0.31)	<0.001
Polymethylation score: coeffcients for sustained smoking from older children peripheral blood meta-analysis (mean-centered)	753	-0.02 (0.23)	0.09 (0.25)	<0.001	746	-0.02 (0.27)	0.07 (0.28)	<0.001
Polymethylation score: coefficients for any smoking from newborn cordblood meta-analysis (mean-centered)	753	-0.04 (0.21)	0.04 (0.19)	<0.001	746	0.01 (0.22)	0.09 (0.22)	<0.001
AHRR gene: percent cg05575921 methylation	753	77.8 (5.2)	76.8 (5.6)	0.047	746	77 (6)	76 (6)	0.2
MYO1G: cg04180046	753	35 (7)	39 (8)	<0.001	746	35 (8)	38 (8)	<0.001
CYP1A1: cg05549655	753	18.7 (5.1)	20.9 (5.5)	<0.001	746	18.2 (5.2)	20.5 (5.1)	<0.001
GFI1: cg14179389	753	5.67 (2.81)	4.89 (2.62)	0.001	746	5.73 (2.87)	4.73 (1.79)	<0.001
MYO1G: cg22132788	753	69 (10)	73 (9)	<0.001	746	67 (11)	70 (12)	0.006
1 Mean (SD) 2 Welch Two Sample t-test

Supplemental Figure 4: Sensitivity analyses for controlling for different variable sets in multivariable analyses of prenatal maternal smoking and DNA methylation summary measures. Base model: Child sex, maternal income to poverty ratio, immune cell proportion, plate, 1st two principal components from PCA on child genetic data, child age. Prenatal exposures model: base model + yes/no any prenatal maternal alcohol use, yes/no any prenatal other drug use. Secondhand smoking models: prenatal exposures model + yes/no any postnatal maternal/primary care giver smoking at age 1 or 5, pk/day in month prior to primary caregiver/maternal interview at age 9 or 15. Surrogate variable: including all surrogate variables

Supplemental Figure 5 DNA methylation summary measures across combinations of exposure to prenatal and postnatal maternal smoking. Sample size is shown at the bottom of violin plots with captured boxplots. POlymethylation score shown in top facets, percent DNA methylation at cg05575921 in AHRR gene shown in bottom facets, age 9 samples shown in left facets, age 15 shown in right facets

Supplemental Figure 6: Heatmap of P values from Pearson correlations between known covariates and surrogate variables from surrogate variable models

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##   2

Supplemental Table 3: Coefficients for multivariable models of prenatal maternal smoke exposure regressed on selected DNA methylation summary variables (outcomes) among children in the Fragile Families and Child Wellbeing study using surrogate variables

Characteristic	Global methylation				Pediatric clock				Sustained smoking polymethylation score (newborns, cell-type controlled)				AHRR: cg05575921
	N	Beta	95% CI1	p-value	N	Beta	95% CI1	p-value	N	Beta	95% CI1	p-value	N	Beta	95% CI1	p-value
African ancestry
Prenatal maternal smoke exposed	904	0.01	0.01, 0.02	<0.001	904	-0.21	-0.40, -0.02	0.032	904	0.41	0.31, 0.51	<0.001	904	-1.0	-1.5, -0.55	<0.001
European ancestry
Prenatal maternal smoke exposed	235	0.01	0.01, 0.02	<0.001	235	0.03	-0.18, 0.25	0.8	235	0.60	0.39, 0.81	<0.001	235	-1.2	-1.9, -0.41	0.003
Hispanic ancestry
Prenatal maternal smoke exposed	360	0.00	-0.01, 0.01	0.4	360	-0.05	-0.38, 0.28	0.8	360	0.36	0.16, 0.56	<0.001	360	-0.55	-1.5, 0.39	0.2
Unstratified
Prenatal maternal smoke exposed	1499	0.01	0.01, 0.02	<0.001	1499	-0.17	-0.31, -0.03	0.020	1499	0.42	0.34, 0.50	<0.001	1499	-0.92	-1.3, -0.54	<0.001
1 CI = Confidence Interval

Supplemental Table 4: Associations between prenatal maternal smoking and DNA methylation summary measures in multivariable linear models stratified by age or in multivariable linear mixed effect models among 809 US children. All models controlled for: first two principal components of child genetic ancestry (recalculated within ancestry strata for stratified models), child sex, maternal income-to-poverty ratio at birth, immune cell proportion estimated from methylation data, child age

Characteristic	Global methylation				Pediatric clock				Sustained smoking polymethylation score (newborns, cell-type controlled)				AHRR: cg05575921
	N	Beta	95% CI1	p-value	N	Beta	95% CI1	p-value	N	Beta	95% CI1	p-value	N	Beta	95% CI1	p-value
Age 9 models
Prenatal maternal smoke exposed	753	0.02	-0.08, 0.12	0.6	753	-0.07	-0.18, 0.04	0.2	753	0.52	0.36, 0.67	<0.001	753	-1.0	-1.7, -0.35	0.003
Age 15 models
Prenatal maternal smoke exposed	746	0.09	-0.02, 0.20	0.12	746	-0.04	-0.24, 0.16	0.7	746	0.46	0.30, 0.62	<0.001	746	-0.80	-1.6, -0.02	0.043
Longitudinal models
Prenatal maternal smoke exposed	1499	0.05	-0.03, 0.14	0.2	1499	-0.02	-0.16, 0.11	0.7	1499	0.48	0.34, 0.62	<0.001	1499	-0.92	-1.5, -0.35	0.002
1 CI = Confidence Interval

Supplemental Table 5: Associations between prenatal maternal smoking and DNA methylation summary measures in multivariable models among 809 US children by ancestry using linear mixed effect models. All models controlled for: first two principal components of child genetic ancestry (recalculated within ancestry strata for stratified models), child sex, maternal income-to-poverty ratio at birth, immune cell proportion estimated from methylation data, child age

Characteristic	Global methylation				Pediatric clock				Sustained smoking polymethylation score (newborns, cell-type controlled)				AHRR: cg05575921
	N	Beta	95% CI1	p-value	N	Beta	95% CI1	p-value	N	Beta	95% CI1	p-value	N	Beta	95% CI1	p-value
African ancestry
Prenatal maternal smoke exposed	904	0.05	-0.05, 0.16	0.3	904	0.05	-0.13, 0.22	0.6	904	0.53	0.34, 0.71	<0.001	904	-1.2	-1.9, -0.46	0.001
European ancestry
Prenatal maternal smoke exposed	235	-0.07	-0.27, 0.12	0.5	235	0.01	-0.24, 0.25	>0.9	235	0.41	0.04, 0.77	0.030	235	-1.2	-2.5, 0.01	0.052
Hispanic ancestry
Prenatal maternal smoke exposed	360	0.11	-0.10, 0.31	0.3	360	-0.28	-0.63, 0.06	0.11	360	0.25	-0.08, 0.58	0.13	360	0.30	-1.1, 1.7	0.7
Unstratified
Prenatal maternal smoke exposed	1499	0.05	-0.03, 0.14	0.2	1499	-0.02	-0.16, 0.11	0.7	1499	0.48	0.34, 0.62	<0.001	1499	-0.92	-1.5, -0.35	0.002
1 CI = Confidence Interval

Supplemental Figure 7: Associations between prenatal maternal smoking and polymethylation scores calculated using alternative coefficient sets among n n_total children in the Fragile Families and Child Wellbeing study. Base model: Child sex, maternal income to poverty ratio, immune cell proportion, plate, 1st two principal components from PCA on child genetic data, child age. Prenatal exposures model: base model + yes/no any prenatal maternal alcohol use, yes/no any prenatal other drug use. Secondhand smoking models: prenatal exposures model + yes/no any postnatal maternal/primary care giver smoking at age 1 or 5, pk/day in month prior to primary caregiver/maternal interview at age 9 or 15. Surrogate variable: including all surrogate variables

Supplemental Figure 8 - Associations between prenatal maternal smoking and other a priori CpG sites selected from previous meta-analyses among 809 children in the Fragile Families and Child Wellbeing study

Supplemental Table 6: Area under the curve for models shown in Main Figure 4 for classifying prenatal maternal smoke exposure, with P value when comparing to base model only or to model using polymethylation score + base model. Base model: Child sex, maternal income to poverty ratio, immune cell proportion, plate, 1st two principal components from PCA on child genetic data, child age.

Age	Model	AUC	P value vs base model	P value vs base model + polymethylation score
Age 9	Global methylation	0.53	0.0000	0.0000
Age 9	Sustained smoking polymethylation score (newborns, cell-type controlled)	0.66	0.0514	0.0000
Age 9	AHRR: cg05575921	0.55	0.0000	0.0000
Age 9	Base model+No methylation	0.73	1.0000	0.0003
Age 9	Base model+Global methylation	0.73	0.3522	0.0004
Age 9	Base model+Sustained smoking polymethylation score (newborns, cell-type controlled)	0.77	0.0003	1.0000
Age 9	Base model+AHRR: cg05575921	0.74	0.1639	0.0256
Age 15	Global methylation	0.54	0.0000	0.0000
Age 15	Sustained smoking polymethylation score (newborns, cell-type controlled)	0.65	0.0274	0.0000
Age 15	AHRR: cg05575921	0.53	0.0000	0.0000
Age 15	Base model+No methylation	0.72	1.0000	0.0008
Age 15	Base model+Global methylation	0.72	0.3976	0.0008
Age 15	Base model+Sustained smoking polymethylation score (newborns, cell-type controlled)	0.77	0.0008	1.0000
Age 15	Base model+AHRR: cg05575921	0.73	0.4670	0.0056

Supplemental Table 7: Area under the curve when using different coefficient sets to construct polymethylation scores for predicting prenatal maternal smoke exposure. With P value when comparing to base model only or to model using polymethylation score + base model. Base model: Child sex, maternal income to poverty ratio, immune cell proportion, plate, 1st two principal components from PCA on child genetic data, child age.

Age	Model	AUC	P value vs base model	P value vs base model + polymethylation score with cell-type control
Age 9	Any smoking polymethylation score (newborns)	0.6197	0.0010	0.0000
Age 9	Sustained smoking polymethylation score (newborns, cell-type controlled)	0.6650	0.0514	0.0000
Age 9	Sustained smoking polymethylation score (newborns)	0.6178	0.0008	0.0000
Age 9	Sustained smoking polymethylation score (older children)	0.6333	0.0037	0.0000
Age 9	Base model+No methylation	0.7260	1.0000	0.0003
Age 9	Base model+Any smoking polymethylation score (newborns)	0.7597	0.0033	0.0117
Age 9	Base model+Sustained smoking polymethylation score (newborns, cell-type controlled)	0.7741	0.0003	1.0000
Age 9	Base model+Sustained smoking polymethylation score (newborns)	0.7596	0.0032	0.0120
Age 9	Base model+Sustained smoking polymethylation score (older children)	0.7676	0.0009	0.4602
Age 15	Any smoking polymethylation score (newborns)	0.6062	0.0007	0.0000
Age 15	Sustained smoking polymethylation score (newborns, cell-type controlled)	0.6471	0.0274	0.0000
Age 15	Sustained smoking polymethylation score (newborns)	0.6054	0.0006	0.0000
Age 15	Sustained smoking polymethylation score (older children)	0.5921	0.0002	0.0000
Age 15	Base model+No methylation	0.7213	1.0000	0.0008
Age 15	Base model+Any smoking polymethylation score (newborns)	0.7565	0.0012	0.0966
Age 15	Base model+Sustained smoking polymethylation score (newborns, cell-type controlled)	0.7669	0.0008	1.0000
Age 15	Base model+Sustained smoking polymethylation score (newborns)	0.7566	0.0012	0.1073
Age 15	Base model+Sustained smoking polymethylation score (older children)	0.7533	0.0078	0.1022